[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

Wibowo Arindrarto w.arindrarto at gmail.com
Fri Feb 1 10:29:59 UTC 2013

Hi Michiel, Peter, everyone,

>> > I'm OK with using the setUp and tearDown arguments to
>> > doctest.DocTestSuite to do the directory magic, but
>> keeping the test files
>> > under Tests/.
>> As a more elegant version of the Bio._utils.run_doctest()
>> function?
> Exactly. Bow, do you want to give this approach a try? (Assuming that there are no further objections from the other developers).

Just to be clear, we are:

* changing all module's doctest file path to use relative paths (with
respect to the module's location),
* replacing the run_doctest() import with a simpler doctest import and
`doctest.testmod()` in each module having this doctest
* resorting to setUp and tearDown in the DocTestSuite in
`run_tests.py` so that each module / submodule can find their test
* and refactoring all string functions in Bio._utils to Bio.Phylo and
Bio.SearchIO, so that we can remove Bio._utils,


I'd be happy to give this a shot if everyone feels the same :).


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